GENEALOGY-DNA-L Archives

From:
Subject: [DNA] Skin pigmentation
Date: Sat, 3 May 2003 14:22:17 EDT

There is an article by Mark Shriver et al "Skin pigmentation, biogeographical
ancestry, and admixture mapping" with more background. This paper will be of
interest to anyone who wants to delve into the methods used for the Ancestry
by DNA test.

This URL ends with .pdf in case RootsWeb splits it:

http://www.erin.utoronto.ca/~eparra/profile/PDF%20files/Shriver%20et%20al.,%20

2003.pdf

Your Ancestry by DNA report has a file called Sequences.pdf which contains
the "reference sequence" (rs) number of 9 of the markers used (labelled
#1139, #1121, etc. in your genotypes file). Everyone gets the same sequences
report -- it's meant to illustrate what a sequence looks like and allows you
to look up details about some of the markers. In past messages I worked
through marker #1122, close to the LPL (LipoProtein Lipase) gene. If you
search the archives for LPL you'll find those messages.

There is a SNP database located at http://www.ncbi.nlm.nih.gov/SNP/. I
cross-referenced the rs numbers with the dbSNP numbers used in Shriver's
paper, Table 1:

#1139 = 4387024
#1121 = 4387029
#1136 = 4387031
#1141 = 4387041
#1116 = 4387033
#1122 = 4387026
#1138 = 4387036
#1128 = 4387023
#1113 = 4387022

I'm still studying this paper myself, but I'd like everyone to take note of
Table 1, with columns for percentages of the SNP found in African, European,
or Native American populations. You'll see that there is no marker with
occurs in 100% of one population and 0% of the other populations. That is one
of the factors which makes the Ancestry by DNA test "fuzzy" -- so you have
confidence intervals around your Maximum Likelihood Estimate (MLE). However,
these markers were selected because the frequency does vary substantially,
and when you look at them in combination, the evidence accumulates for a
certain biogeographical ancestry.

Ann Turner - GENEALOGY-DNA List Administrator
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